I'm sorry if this has previously been asked, but I was unable to find anything pertaining to it.

I encoded a WAV into FLAC and calculated the MD5 for each and converted it back. Both WAV files had the same checksum, but when I did --show-md5sum it gave me a compltely different value, that value didnt match the FLAC or the WAV.

If the result of the --show-md5sum is supposed to be different what is that hash calculated from?

Would you like to give some more informations regarding your software?

I encoded it originally with the Convert To in foobar and decoded it the same way. I did it again with Flac front end and got the same results. The checksum was created with Hash Tab and wxChecksums and both of those came out the same.